GapMind for catabolism of small carbon sources

 

Aligments for a candidate for livM in Azospirillum brasilense Sp245

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate AZOBR_RS08240 AZOBR_RS08240 ABC transporter permease

Query= uniprot:A0A165KER0
         (358 letters)



>lcl|FitnessBrowser__azobra:AZOBR_RS08240 AZOBR_RS08240 ABC
           transporter permease
          Length = 505

 Score =  246 bits (629), Expect = 7e-70
 Identities = 147/325 (45%), Positives = 191/325 (58%), Gaps = 45/325 (13%)

Query: 32  IADLALLYVLLALGLNIVVGYAGLLDLGYVAFYAVGAYLFALMASPHLADNFAAFAAMFP 91
           I  L L Y++L  GLNIVVG AGLLDLGYVAFYAVGAY +AL+A      ++  F     
Sbjct: 175 IGILLLTYIMLGWGLNIVVGLAGLLDLGYVAFYAVGAYSYALLA------HYFGF----- 223

Query: 92  NGLHTSLWIVIPVAALLAAFFGAMLGAPTLKLRGDYLAIVTLGFGEIIRIFLNNLDHPVN 151
                S W+ +P+A  LAA  G +LG P L+LRGDY AIVTLGFGEIIRI L N      
Sbjct: 224 -----SFWVCLPLAGFLAAMSGVLLGFPVLRLRGDYFAIVTLGFGEIIRIILINW---YQ 275

Query: 152 LTNGPKGLGQIDSVKVFGLDLGKRL---------EVFGFD---INSVTLYYYLFLVLVVV 199
            T GP G+  I     FG+    R          E+FG +   ++ +   YYL LVL +V
Sbjct: 276 FTGGPNGISGIPRPSFFGIADFTRTPAEGTAAFHEMFGLEFSPLHRIIFLYYLILVLALV 335

Query: 200 SVIICYRLQDSRIGRAWMAIREDEIAAKAMGINTRNMKLLAFGMGASFGGVSGAMFGAFQ 259
             +   R++   +GRAW A+RED+IA  ++GIN  NMKL AF + A FGG +G+ F   Q
Sbjct: 336 VNLFTMRVRKLPLGRAWEALREDDIACASLGINRTNMKLAAFAIAAMFGGFAGSFFATRQ 395

Query: 260 GFVSPESFSLMESVMIVAMVVLGGIGHIPGVILGAVLLSALPEVLRYVAGPLQAMTDGRL 319
           GF+SPESF+ +ES +I+A+VVLGG+G   GV++ A L+  LPE  R +A           
Sbjct: 396 GFISPESFTFIESAIILAIVVLGGMGSQIGVVVAAFLVIGLPEAFRELAD---------- 445

Query: 320 DSAILRQLLIALAMIIIMLLRPRGL 344
                R L   + M++IML RPRGL
Sbjct: 446 ----YRMLAFGMGMVLIMLWRPRGL 466


Lambda     K      H
   0.328    0.144    0.430 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 469
Number of extensions: 25
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 358
Length of database: 505
Length adjustment: 32
Effective length of query: 326
Effective length of database: 473
Effective search space:   154198
Effective search space used:   154198
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 51 (24.3 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory